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Key Skills

BioC Bioconductor (DESeq2, edgeR)

Main

James Sacco

Bioinformatics Scientist
Department of Gene and Cell Therapy
ASC Therapeutics
Milpitas, CA 95035

Independent, self-motivated bioinformatics scientist, with six years of combined experience in cancer immunotherapy and gene therapy. Specialist in computational biology of CRISPR gene editing. An analytical thinker and quick learner, with experience in next-generation sequencing (NGS) methods, such as RNA-Seq, and development of reproducible, robust pipelines.

Integrated genotype-phenotype data to predict disease severity. Developed machine learning applications to analyze population-scale genomics and real-world patient data.


Experience

Bioinformatics Scientist

ASC ASC Therapeutics (Contract)

Milpitas, CA

Present - 2021

● Quantify and characterize CRISPR gene modifications, with both custom and open-source tools for genomic data analysis.

● Query, retrieve, and integrate data from public genomics databases, to enhance on-target gene editing with sequence alignment protocols.

● Examine concordance and sensitivity of five open-source CRISPR off-target detection methods (CALITAS, CHANGE-Seq, CRISPResso, GUIDE-Seq, and Cas-OFFinder).

● Streamline high-performance analyses for bench scientists by constructing custom data pipelines, command line tools, and user interfaces.

● Generate reproducible reports for publication-quality manuscripts.

Biomarker Data Analyst II

GNE Genentech (Contract)

South San Francisco, CA

2020 - 2019

● Established department-first machine learning pipeline to study effects of biomarker operations on quality of cancer immunotherapy assays.

● Upgraded data operations for six data streams, including flow cytometry, biomarker operations, and oncology data warehouses.

● Monitored and solved sample data quality issues for two cancer immunotherapy trial arms.

Data Curator

GNE Genentech (Contract)

South San Francisco, CA

2019 - 2018

● Collaborated with AI engineers to create an ETL pipeline for multi-modal survival prediction and patient stratification, by using Python ML and R to integrate gene panel and RNA-Seq data.

● Designed ETL data pipeline for integration of real-world EHRs into deep learning module, using Python, SQL, and Apache Spark.

● Organized and managed close coordination of Artificial Intelligence, data management, and DevOps functions, to bring clinical machine learning from prototype to production.

PROGRAMMING SKILLS

R

Python

Linux

Git

GitHub

Markdown

Dash

C++ C++

MATLAB MATLAB

LANGUAGES

English: Native

Spanish: Bilingual Proficiency

Active member of Biostars

I have participated in bioinformatics and software workshops and Meetup.com groups, in both Seattle, WA and San Francisco, CA, including:

SF/Bay AI Developers Group

San Jose Data Science and AI/ML Meetup

Hacker Dojo

Seattle Sequencing

:::

Data Curator, Bioinformatics Analyst

BioMarin BioMarin Pharmaceutical (Contract)

San Rafael, CA

2018 - 2017

● Established an integrated genetic and curated literature workflow to predict incidence and prevalence rates of over sixty rare, genetic disorders, with statistical and data visualization R packages (ggplot2) and MATLAB.

● Upgraded and tested RNA-Seq data pipeline (STAR2, SAMtools, Bioconductor) to discern disease contribution of rare variants to neural disease.

● Spearheaded development of three relational databases derived from Hail population genomics platform, in collaboration with software engineer.

● Co-authored manuscript submitted to peer-reviewed publication, on prediction of disease severity in metachromatic leukodystrophy.

● Developed allele-specific association models and GWAS analysis software for two later published manuscripts.

Research Associate

UM Pearse Lab: The Miami Project to Cure Paralysis, The Miller School of Medicine, University of Miami

Miami, FL

2017 - 2016

● Mentored research associates in developing bioinformatic skills, specifically in multiple sequence alignment and standard molecular biological protocols (restriction enzyme digestion, gel electrophoresis, spectrophotometry).

● Identified over forty putative conserved vertebrate phosphodiesterase proteins, by using multiple sequence alignment and genomic evidence.

Education

Rowan University, Graduate School of Biomedical Sciences

Master of Biomedical Science (Distinction)

Stratford, NJ

N/A

“Hippocampal long-term potentiation in neurodegenerative disorders”

Florida International University, The Honors College

BSc, Biological Sciences

Miami, FL

Professional Development

Introduction to Genomic Technologies

Johns Hopkins University

Online

2021

Statistics for Genomic Data Science

Johns Hopkins University

Online

2021

Software Carpentry for R and UNIX

University of Miami

Miami, FL

2016

Publications

Regulating Axonal Responses to Injury: The Intersection between Signaling Pathways Involved in Axon Myelination and The Inhibition of Axon Regeneration.

Frontiers in Molecular Neuroscience. 2016 Jun 8;9:33.

N/A

2016

Rao S.N., Pearse D.D. Manuscript Editor

Conference Papers

Prediction of disease severity in metachromatic leukodystrophy using measures of protein activity and a novel phenotype matrix.

American Society of Human Genetics American Society of Human Genetics Virtual Meeting. [Poster] [Forthcoming on bioRxiv.org]

Online

2020

Trinidad M., Hong X., Sacco J., Nguyen H.P., Clark W.T., Froelich S., LeBowitz J.H., Gelb M.H.

Association of HGMD and gnomAD variants of unknown significance with prediction of disease incidence and prevalence.

BioMarin BioMarin Internal Research and Development Asilomar Conference. [Poster]

Pacific Grove, CA

2018

Sacco J., Clark W.T., Yu K., Wu K., LeBowitz J.H.

Research Projects

Characterization of glycan substrates accumulating in GM1 gangliosidosis

Molecular Genetics and Metabolism Reports. 2019. 21, p.100524.

N/A

2019

Lawrence R., et al.

Utilizing ExAC to assess the hidden contribution of variants of unknown significance to Sanfilippo Type B incidence

PLoS One. 2018. 13(7):e0200008.

N/A

2018

Clark W.T., et al.

EXTRA-CURRICULAR

Ultimate frisbee at Big Gay Frisbee. San Francisco, CA. 2018 – Present.

Salsa dance at In Lak’ech Dance Academy. Oakland, CA. 2019.

Rugby at Seattle Quake RFC. Seattle, WA. 2016 – 2017.

Phosphodiesterase Inhibitors as a Therapeutic Approach to Neuroprotection and Repair

International Journal of Molecular Sciences. 2017. 18(4): 696.

N/A

2017

Knott E.P., et al.

Presentations

Data Visualization of RNA-Seq Differential Expression Analysis with DESeq2

HHMI Doudna Lab: Howard Hughes Medical Institute, Department of Molecular and Cell Biology, University of California, Berkeley

Berkeley, CA

2022

Topics: Introduction to RNA-Seq, Standard Workflows with DESeq2, Reference-Based Assembly, Exploratory Data Analysis, Statistical Analysis, Data Visualization, Gene Set Enrichment, Variant Annotation

● Presented publication-quality RNA-Seq data summaries and representations to post-doctoral associates

Teaching

Peer-Led Team Learning

Florida International University

Miami, FL

2009

General Biology II facilitator for two concurrent PLTL courses

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Last update: 2022-02-10.The most recent version of this resume is available here.